Set after Shrek Forever After, Puss in Boots hosts a party in a governor's mansion in the Spanish town of Del Mar when a giant attacks them. He manages to defeat it but is crushed by a bell shortly after. Waking up, he is informed by a Doctor that he only has one life left after dying eight times before.note Puss initially brushes it off, but after getting scarred and nearly killed in a duel with a black-hooded wolf in a local pub that night, he reluctantly goes to the house of Mama Luna, an elderly cat lady, to be a domesticated pet. He buries his outfit in the garden.
Months later, Puss has grown a beard and meets an optimistic Chihuahua disguised as a cat, whom he calls Perrito. Goldilocks and her Three Bears Crime Family soon arrive at Luna's home, looking to hire Puss to help them steal a map bearing the Wishing Star's location, but fail to recognize him, and leave after finding his "grave". Puss decides to use the Star to restore his lost lives.
Accompanied by Perrito, Puss travels to the factory lair of corrupt pastry salesman and magical artifact collector "Big" Jack Horner, who intends to use the Star to control all the magic in the world. Puss finds the map, but is interrupted by his resentful ex-fiancée Kitty Softpaws. Goldi, the Bears, and Horner arrive on the scene; Puss, Perrito and Kitty escape with the map, but Puss sees the Wolf behind them in the distance.
The map leads the trio to the Dark Forest, a pocket dimension that changes its appearance depending on the map's holder. The dimension transforms into a hellish setting for Puss and Kitty, while Perrito is given a nice setting. Puss, Kitty, Jack, and Goldi are all stalled by a forest of ravenous flowers. Puss and Kitty are able to show kindness and pass, while Jack is forced to fight the flowers. While he does so, he frees a magical Ethical Bug who seeks to show kindness to all. While riding downstream, Puss gets his beard shaved off by Kitty before getting rid of a stick which Perrito follows, leading to the latter being captured by Jack. Mid-fight, Puss sees the hooded wolf again and runs off in fear, distracting Kitty and enabling Goldi to obtain the map.
After Perrito calms Puss' ensuing panic attack, Puss confesses his fears, and his remorse for abandoning Kitty just before their wedding. Kitty overhears the conversation and reveals that she never came to the altar either, feeling like she could never compete with someone who loves himself more than her.
Puss and Kitty retrieve the map while Goldi and the Bears are distracted by a manifestation of their woodland cottage, though they manage to kidnap Perrito and take him hostage. As the dimension shifts, Puss accidentally traps himself in the Cave of Lost Souls, where he encounters his arrogant past eight lives, and the Wolf, who reveals himself as Death. Offended by Puss' failure to value his extra lives, Death intends to take Puss' final life prematurely. Horrified, Puss runs out of the cave towards the Star alone, leaving Kitty and Perrito behind. Meanwhile, Goldi reveals to the Bears that her wish is to be reunited with her biological family; although devastated, the Bears agree to help her. Jack’s ruthlessness leads to the death of nearly all of his minions, and the Ethical Bug finally sees that he is totally heartless before Jack flicks him away.
Finally reaching the star, Puss is about to make his wish but is stopped by Kitty, who calls him out for his selfishness and confesses that her wish was to find someone she could trust. Shortly after, they are interrupted by Goldi, the bears and Jack. A fight ensues, during which Jack is thrown into his never-ending nanny bag by Kitty and Goldi saves Baby when he is almost thrown off the star.
Death arrives and challenges Puss to a duel. Having learned the value of life from his time with his companions, Puss forgoes wishing for more lives and accepts, temporarily disarming the Wolf. Puss declares that he knows he can never defeat Death, but he will never stop fighting for his last life. Seeing that Puss has lost his arrogance, Death begrudgingly decides to spare him. Puss and Death acknowledge that they will eventually meet again one day, and Death disappears. Puss reconciles with Kitty and gives her the map, but she doesn't need it.
Jack re-emerges from his bag, having eaten a cookie that makes him grow big, and seizes the map from Puss and Kitty. As Jack attemps to make a wish, however, Perrito manages to distract him long enough for Puss, Kitty and Goldi to reclaim the map and rip it to shreds, causing the Wishing Star to collapse and kill Jack after it violently implodes when he attempts to reassemble the map, being stopped by the Ethical Bug and a phoenix he brought with him burning it to ensure he cannot finish his wish.
In the aftermath, Goldi finally accepts being a part of the bear family and they leave to take over Horner's bakery, with the Ethical Bug joining them. Puss and Kitty rekindle their relationship. Perrito also finally gets his name, sticking with Perrito and saying it suits him. Sometime later, Puss, Kitty and Perrito (now wanted as "Team Friendship") steal a boat from the Governor and set sail to reunite with "some old friends" at the Kingdom of Far Far Away.
